Great project!! I always wanted the bigger SS 18, absolutely loved my SS 16 all the way till the end, RIP.
Yeah, don't let the project spook you or slow you down. The transom is a 'big deal' but like said above, it really is just 1 weekend of focused work. I cut and installed mine in my 25 foot aluminum Starcraft with relative ease. Used ACX or BCX, titebond 3 glue, screws to pin it all together, and rustoleum. Great results

and easy install. This is one of the exact advantages to these simple aluminum boats- the transom is Not glassed in = cheap easy replacement. Tip: If you have a router- taking the corners off with a quarter round helps protect the finish and helps the new transom slide into place a little easier/less binding. I ran the router across all the edges but the top for this reason. Great thing about regular old paint is if you scrape the paint a little installing it- it's easy and plenty cheap to touch up after with your extra left over. No elaborate prep needed for paint, just basic prep. And it soaks in pretty damn good in my opinion! I used rustoleum alkyd enamel floor and patio paint on my 5/8 BCX decks with the traction compound.
Yeah epoxy IS the best, blah, blah, not arguing that. Or you can be an ass like me and proudly use none on your boat, just like from the SC factory!

I was really impressed with the lifespan of the original used and abused basic stuff so I definitely don't coat things with 75 plus dollar a gallon tempermental crap that needs 15 weekends to be "right". Cheap boats don't need to be treated like they're Hinckleys or something. The oil based rustoleum will give you serious bang for the buck and last a very long time with little care. Esp if you cover your boat when not un use, then it will basically last forever. Leaves and rain kill em slowly and quietly while they wait to be used. Keep it clean and nose tilted significantly up to keep decks drained and everything goes out drain plug hole like it'ssupposed to. This makes a huge difference.
Best of luck with it and if you want any pictures of the exact process I have a bunch I can send you or they're prob in my chief 25 build thread.